Without a clearance he can't do his job anymore and he'll either be let go or at least transferred to some Severance (2022) hellhole.

I guess it was a previous whistleblower(?) that claimed a $22 million dollar secret program to investigate UFOs - that's chump change for a secret program. That'll pay for a SCIF and a couple of clearances, maybe per diem and a few trips to investigate crop circles.

Joking aside that's a comically small amount for the government to investigate non-human craft. If there were really alien craft with dead pilots we'd be spending many billions investigating them using all the science available.